LAMMPS (15 Apr 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
  using 1 OpenMP thread(s) per MPI task
# two monomer nylon example
# reaction produces a condensed water molecule

units real

boundary p p p

atom_style full

kspace_style pppm 1.0e-4

pair_style lj/class2/coul/long 8.5

angle_style class2

bond_style class2

dihedral_style class2

improper_style class2

read_data tiny_nylon.data
  orthogonal box = (-25 -25 -25) to (25 25 25)
  1 by 2 by 2 MPI processor grid
  reading atoms ...
  44 atoms
  reading velocities ...
  44 velocities
  scanning bonds ...
  9 = max bonds/atom
  scanning angles ...
  21 = max angles/atom
  scanning dihedrals ...
  29 = max dihedrals/atom
  scanning impropers ...
  29 = max impropers/atom
  reading bonds ...
  42 bonds
  reading angles ...
  74 angles
  reading dihedrals ...
  100 dihedrals
  reading impropers ...
  44 impropers
  4 = max # of 1-2 neighbors
  6 = max # of 1-3 neighbors
  12 = max # of 1-4 neighbors
  41 = max # of special neighbors
  special bonds CPU = 0.000431282 secs
  read_data CPU = 0.0129571 secs

variable runsteps equal 1000
variable prob1 equal step/v_runsteps*2
variable prob2 equal (step/v_runsteps)>0.5

velocity all create 300.0 4928459 dist gaussian

molecule mol1 rxn1_stp1_unreacted.data_template
Read molecule template mol1:
  1 molecules
  18 atoms with max type 8
  16 bonds with max type 14
  25 angles with max type 28
  23 dihedrals with max type 36
  14 impropers with max type 11
molecule mol2 rxn1_stp1_reacted.data_template
Read molecule template mol2:
  1 molecules
  18 atoms with max type 9
  17 bonds with max type 13
  31 angles with max type 27
  39 dihedrals with max type 33
  20 impropers with max type 1
molecule mol3 rxn1_stp2_unreacted.data_template
Read molecule template mol3:
  1 molecules
  15 atoms with max type 9
  14 bonds with max type 13
  25 angles with max type 27
  30 dihedrals with max type 33
  16 impropers with max type 1
molecule mol4 rxn1_stp2_reacted.data_template
Read molecule template mol4:
  1 molecules
  15 atoms with max type 11
  13 bonds with max type 15
  19 angles with max type 29
  16 dihedrals with max type 32
  10 impropers with max type 13

thermo 50

# dump 1 all xyz 1 test_vis.xyz

fix myrxns all bond/react stabilization yes statted_grp .03   react rxn1 all 1 0.0 5.0 mol1 mol2 rxn1_stp1_map prob v_prob1 1234   react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map prob v_prob2 1234
WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (src/USER-REACTION/fix_bond_react.cpp:2051)
WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (src/USER-REACTION/fix_bond_react.cpp:2051)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined

fix 1 statted_grp_REACT nvt temp 300 300 100

# optionally, you can customize behavior of reacting atoms,
# by using the internally-created 'bond_react_MASTER_group', like so:
fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1

thermo_style custom step temp press density v_prob1 v_prob2 f_myrxns[1] f_myrxns[2]

# restart 100 restart1 restart2

run ${runsteps}
run 1000
PPPM initialization ...
  using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
  G vector (1/distance) = 0.0534597
  grid = 2 2 2
  stencil order = 5
  estimated absolute RMS force accuracy = 0.0402256
  estimated relative force accuracy = 0.000121138
  using double precision FFTW3
  3d grid and FFT values/proc = 252 2
Neighbor list info ...
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 10.5
  ghost atom cutoff = 10.5
  binsize = 5.25, bins = 10 10 10
  2 neighbor lists, perpetual/occasional/extra = 1 1 0
  (1) pair lj/class2/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d/newton
      bin: standard
  (2) fix bond/react, occasional, copy from (1)
      attributes: half, newton on
      pair build: copy
      stencil: none
      bin: none
WARNING: Inconsistent image flags (src/domain.cpp:812)
Per MPI rank memory allocation (min/avg/max) = 33.66 | 33.88 | 34.43 Mbytes
Step Temp Press Density v_prob1 v_prob2 f_myrxns[1] f_myrxns[2] 
       0          300    346.78165 0.0034851739            0            0            0            0 
      50     266.5092   -90.813802 0.0034851739          0.1            0            1            0 
     100    559.41271    -53.23688 0.0034851739          0.2            0            1            0 
     150    489.90516    31.555817 0.0034851739          0.3            0            1            0 
     200    326.18391    7.7889992 0.0034851739          0.4            0            1            0 
     250    339.78203    2.3919541 0.0034851739          0.5            0            1            0 
     300    370.90263    -32.01673 0.0034851739          0.6            0            1            0 
     350    294.07547   -5.4019813 0.0034851739          0.7            0            1            0 
     400    287.76477    12.254133 0.0034851739          0.8            0            1            0 
     450    293.36482    66.372956 0.0034851739          0.9            0            1            0 
     500    246.84496    26.132317 0.0034851739            1            0            1            0 
     550    253.08778   -15.350262 0.0034851739          1.1            1            1            1 
     600    358.83641    25.007371 0.0034851739          1.2            1            1            1 
     650    320.51492    -32.34823 0.0034851739          1.3            1            1            1 
     700    310.87976   -8.2306669 0.0034851739          1.4            1            1            1 
     750    307.54142    12.025818 0.0034851739          1.5            1            1            1 
     800    272.51724    -22.92823 0.0034851739          1.6            1            1            1 
     850    268.66181    10.069534 0.0034851739          1.7            1            1            1 
     900     265.5531   -10.471377 0.0034851739          1.8            1            1            1 
     950    259.43086    9.4546712 0.0034851739          1.9            1            1            1 
    1000    247.14622    20.250308 0.0034851739            2            1            1            1 
Loop time of 0.357762 on 4 procs for 1000 steps with 44 atoms

Performance: 241.502 ns/day, 0.099 hours/ns, 2795.157 timesteps/s
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.0003917  | 0.015545   | 0.033317   |  11.9 |  4.35
Bond    | 0.0010131  | 0.030153   | 0.076975   |  18.2 |  8.43
Kspace  | 0.092857   | 0.1462     | 0.18688    |  10.7 | 40.87
Neigh   | 0.043786   | 0.044014   | 0.044189   |   0.1 | 12.30
Comm    | 0.03636    | 0.038345   | 0.040538   |   0.8 | 10.72
Output  | 0.00091578 | 0.0012541  | 0.0020923  |   1.4 |  0.35
Modify  | 0.075379   | 0.080791   | 0.086052   |   1.8 | 22.58
Other   |            | 0.00146    |            |       |  0.41

Nlocal:    11 ave 32 max 0 min
Histogram: 2 0 1 0 0 0 0 0 0 1
Nghost:    40 ave 51 max 19 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Neighs:    191 ave 529 max 0 min
Histogram: 2 0 0 0 1 0 0 0 0 1

Total # of neighbors = 764
Ave neighs/atom = 17.3636
Ave special neighs/atom = 9.77273
Neighbor list builds = 1000
Dangerous builds = 0

# write_restart restart_longrun
# write_data restart_longrun.data

Please see the log.cite file for references relevant to this simulation

Total wall time: 0:00:00
